B. pertussis infects the upper respiratory tract by adhering to ciliated epithelial cells and releasing toxins. The virulence genes that encode these proteins are regulated by the BvgS-BvgA two-component system. The response regulator BvgA binds to the promoter region of all known B. pertussis virulence genes to activate their transcription during infection. These genes include bipA, fha, fim, ptx, prn, cya, bvgR and bvgA itself. The binding pattern of BvgA at each of the virulence gene promoters is of interest because it often differs from the classically described models of prokaryotic transcription activation, termed Class I and Class II. Class I activation involves an interaction between an activator and the alpha-CTDs of RNA polymerase at positions upstream of the core promoter DNA. Class II activation also involves direct contact between the activator and RNA polymerase, but the activator binds close to the promoter -35 element. A full characterization of the mechanism of BvgA activation at the virulence gene promoters is an important step towards controlling the virulence of this pathogen. To understand the transcriptional regulation of the B. pertussis virulence genes, we have begun a collaboration with the laboratory of Dr. Scott Stibitz (Food and Drug Administration), whose work has investigated the mechanism of B. pertussis pathogenicity for many years. The work of Dr. Stibitz's lab has shown that at the B.pertussis fha promoter, BvgA binding and activation exhibits characteristics of both Class I and Class II activation: the alpha-CTDs are required for activation, and the activator binds close to or overlapping the -35 site. Another virulence gene, fim3, appears to have extensive overlap between the BvgA binding site and the core promoter elements, thus resembling a Class II binding pattern. However, the mechanism of BvgA activation of fim3 and the other virulence genes cannot be further illuminated without a biochemical characterization of their promoter regions and promoter elements. To start our collaboration, we have complemented this previous work describing the BvgA binding sites by performing primer extension experiments to identify in vivo transcription start sites at fim3, fhaB, bvgAS, ptx, prn, and cya. This work has allowed us to identify the core promoter elements for each of these genes.